[gmx-users] A question about "blowing up"

[sujithkakkat .]

Hello Justin,

  Thank you for the comments. While following the free energy calculation
in the tutorial, I found that the constrains are switched on , while going
from the minimization procedure to the NVT equilibration and the final
results were pretty accurate. I guess that depends on the type of
calculation and the system studied.

On a side note, I found the value of free energy calculated to be -9.56
kJ/mol instead of -9.25 kJ/mol which you obtained. I am sure I followed
everything as in the tutorial and I am using Gromacs-4.6.5. I hope the
difference is not too worrying.

Regards,

Sujith.


On Sat, Mar 1, 2014 at 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/1/14, 7:22 AM, sujith ks wrote:
>
>> Hello Justin,
>>
>>    I performed energy minimization , the way you performed for the free
>> energy calculation for the methane-water system in the tutorial. In the
>> first step steepest descent was used followed by l-bfgs. The emtol (force)
>> was set to 10 kj/mol/nm.
>>
>> The final results can be summerized as:
>>
>> Low-Memory BFGS Minimizer converged to Fmax < 10 in 7929 steps
>> Potential Energy  = -9.4460383e+04
>> Maximum force     =  7.4954224e+00 on atom 1760
>> Norm of force     =  5.8917433e-01
>>
>> The potential vs time graph looks good (converged).
>>
>>   The .mdp is as follows:
>>
>> ; Run control
>> integrator               = l-bfgs
>> nsteps                   = 100000
>> define                    = -DFLEXIBLE
>> ; EM criteria and other stuff
>> emtol                      = 10
>> emstep                   = 0.01
>> niter                        = 20
>> nbfgscorr                 = 10
>> ; Output control
>> nstlog                      = 1
>> nstenergy                = 1
>> ; Neighborsearching and short-range nonbonded interactions
>> nstlist                     = 1
>> ns_type                  = grid
>> pbc                        = xyz
>> rlist                        = 0.9
>> ; Electrostatics
>> coulombtype              = pme
>> rcoulomb                   = 0.9
>> ; van der Waals
>> vdw-type                 = Cut-off
>> rvdw                       = 1.4
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr                   = EnerPres
>> ; Spacing for the PME/PPPM FFT grid
>> fourierspacing            = 0.12
>> ; EWALD/PME/PPPM parameters
>> pme_order                 = 6
>> ewald_rtol                 = 1e-06
>> epsilon_surface          = 0
>> optimize_fft               = no
>> ; Temperature and pressure coupling are off during EM
>> tcoupl                    = no
>> pcoupl                   = no
>> ; Generate velocities to start
>> gen_vel                  = no
>> ; options for bonds
>> constraints              = none
>> ; Type of constraint algorithm
>> constraint-algorithm     = lincs
>> ; Do not constrain the starting configuration
>> continuation             = no
>> ; Highest order in the expansion of the constraint coupling matrix
>> lincs-order               = 12
>>
>
> This explains why turning off constraints solved the problem.  You
> minimized without any constraints on anything (-DFLEXIBLE and constraints =
> none), but then turned them on during NVT.  What can happen is that a
> configuration that is unconstrained minimizes happily, but the geometry is
> distorted.  You need to run EM under the same conditions that you will use
> for the MD (in terms of constraints).  Minimizing without constraints
> initially is fine if there are problems in the structure, but if you intend
> to constraint anything later, you need to minimize with constraints before
> you can do so.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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